Mitogenome based adaptations and phylogeny of Beetal goats in India

Beetal goats, the second largest Indian goat breed, are known for their adaptation to hot arid tropical climates. Beyond their phylogenetic significance, recent evidence suggests that mitogenome modifications play a crucial role in the adaptation of animals to environmental stress factors. This study aims to characterize the mitogenome of Beetal goats at the molecular level, elucidate their mitogenomic adaptations and determine the maternal phylogenetic status of Indian Beetal goats. Whole genome sequencing of pooled DNA samples from five unrelated Beetal goats was carried out to obtain mitogenome sequence. The Beetal goat mitogenome comprised of a coding region with 37 genes: 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and two ribosomal RNAs (rRNAs), as well as a non-coding hypervariable displacement loop (D-loop) region. We identified nine SNPs inclusive of seven synonymous and two nonsynonymous ones located in PCGs that too in respiratory complex I subunit genes, five of which were novel. Two nonsynonymous SNPs (10,229 A > G in ND4 and 13,964 G > A in ND6 ) were homoplasmic ones with marked influence on their mRNA and protein structures. Synonymous SNPs influenced the minimum free energy (MFE) and topology of predicted mRNA secondary structures, thereby affecting mRNA stability and translation efficiency. Phylogenetic analysis of the D-loop region classified Beetal goats into haplogroup B. Mitogenome analysis of Beetal goats, in comparison with other goat populations revealed the greatest genetic similarity to Southeast Asian goats. The comprehensive analysis of mitochondrial DNA in Beetal goats reveals significant genetic adaptations crucial for their survival in hot, arid environments. This study also highlights the complex matrilineal origins of Beetal goats.